1 Triggers and Settings

2 Import fish and manipulate data a bit

Minimum vis for fish analysis = 2-m

Kelp depths = 5 -m Fish depths = 5, 10 -m Inv depths = 5 -m

Visibility data for 2015 are fake. DI was bad and set at 1.0 m; other sites set at 3.0 m

3 FISH

3.1 Rockfish YOY

## Joining, by = "taxa"

3.2 Fish

Fish depth = 5, 10

## Joining, by = "taxa"

3.3 Fish and YOY plot

4 ALGAE

Kelp depth = 5

## `summarise()` has grouped output by 'year', 'site', 'transect', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone'. You can override using the `.groups` argument.
## Joining, by = "site"

4.1 Canopy kelp

Ole needs to check the definitions of canopy kelp here. I took this from his code, which wasn’t finished.

4.2 Caonopy kelp 5 m only

4.3 Nerocystis at Tatoosh

4.4 Nero and Macro

## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site'. You can override using the `.groups` argument.

4.5 Big three: Nero, Macro, Ptero

Plot the big 3 species: Macro, Nero, Ptero

4.5.1 Big three 5 m only

4.5.2 Big three - Coastwide

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

4.5.3 Coastwide 5m only

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

5 INVERTEBRATES

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'species', 'zone', 'area', 'taxa'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.

5.1 Summed Urchins

Ole will want to clean up the figure

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

5.2 Urchins by species

Probably worth dropping into the supplement to show that it was mostly purple urchins. Partly interesting because there is no purple urchin fishery, but there is a red one. I think.

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

5.3 Seastars

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

Ugly..no aliby..

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

6 COMBINED KELP - URCHIN - SEASTAR PLOTS

6.1 By site and zone

6.2 By year and zone summarized across sites

## `summarise()` has grouped output by 'year', 'zone'. You can override using the `.groups` argument.

6.3 Summarized across sites; 5 m and 10 m depths combined

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

6.4 Summarized across sites; 5-m depth zone only

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

7 Output data for multivariate statistics

7.1 Combine kelp, fish, and inverts for capscale analysis

Not yet transformed to wide format in order to retain SD & SE info upon saving out. Transform in the Multiariate analysis rmd.

Output data files to use for multivariate ordinations.

Use these files and not raw files. Kelp and invert data have been converted to density to account for different transect lengths etc.

8 Quick view of what species to include in kelp ordinations. Basically only the big three have any abundance.

8.1 Algae

## `summarise()` has grouped output by 'species'. You can override using the `.groups` argument.

8.2 Fish

Note, the y-axes are very different

## `summarise()` has grouped output by 'taxa'. You can override using the `.groups` argument.

8.2.1 NOTES

for multivariate analysis; cut and paste to that file

fish.spp = c(“OPEL”, “HEXA”, “SECA”, “SCMA” ,“SENE”, “SEME”, ‘EMBI’,‘GOBI’)

yoy.spp = c(“SECAyoy”, “SEPIyoy”, “SEMYyoy”, “SEBYTyoy”,“RYOY”)